When I access my StackOverflow account I see my rep on Super User is 1 rep.
But when I access Super User I see I had 101 rep.
I don't know why this happens. Can anyone explain why I get these different values?
The "per site" accounts list appears to be cached, as you can see your network profile accounts list show the correct reputation.
More than once I have seen Nick saying something about "reputation events" that triggers cache refresh, so I believe that once you will gain some reputation on Super User it will all be fixed.